AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irhaS_ecoli_bsub_300.orf -g0.5 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 rhaD 300 rhamnulose-phosphate aldolase #2 rhaB_rhaS 287 rhaB: rhamnulokinase, rhaS: positive regulator for rhaBAD operon #3 rhaT 284 rhamnose transport #4 ybfI 230 similar to transcriptional regulator (AraC/XylS family) #5 ycnG 106 similar to 4-aminobutyrate aminotransferase #6 ycnH 68 similar to succinate-semialdehyde dehydrogenase #7 ycxE 122 similar to hypothetical proteins #8 glvA 300 6-phospho-alpha-glucosidase #9 yfiA 64 similar to hypothetical proteins #10 yfiB 105 similar to ABC transporter (ATP-binding protein) #11 yfiD 154 similar to hypothetical proteins #12 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #13 yulE 25 similar to L-rhamnose isomerase #14 yulB 56 similar to transcriptional regulator (DeoR family) #15 yuxG 137 alternate gene name: yulA; similar to sorbitol-6-phosphate 2-dehydrogenase #16 tlpB 113 methyl-accepting chemotaxis protein #17 mcpA 125 methyl-accepting chemotaxis protein #18 tlpA 176 methyl-accepting chemotaxis protein #19 mcpB 157 methyl-accepting chemotaxis protein Motif number 1 CGACGCTGTCGCGTCTTATCAGGC 1 1 0 GCGCATCGGC 0.999531 -300 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 19 1 GCGCATCGGC 0.999555 -282 TAAGGCACTTGTGCCGCATCCGGCAATCAATGCC 1 40 0 GTGCATCGGC 0.997992 -261 TGCGGCACAAGTGCCTTATCCGGCCTACAGGTCG 1 56 1 GTGCATCGGC 0.997992 -245 CGACGCTGTCGCGTCTTATCAGGCCTACAACTGT 1 93 0 GCGCATCGGC 0.999531 -208 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 111 1 GCGCATCGGC 0.999555 -190 ATGCGCACAAGTCGCTTATCAGGCCTACAGGTCG 1 147 1 GTCCATCGGC 0.981408 -154 CGACGCTGTCGCGTCTTATCAGGCCTACAACTAT 1 184 0 GCGCATCGGC 0.999531 -117 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 202 1 GCGCATCGGC 0.999555 -99 ATGCGCGCGAGCGCCTTATCCGGCCTACGGGTCG 1 240 1 GCGCATCGGC 0.999531 -61 AAAAGAGCTGCCGGAAAATCCGGCAGCTCTCAGG 7 24 0 CCGAATCGGC 0.945003 -99 AAACGAGAAAGCGGCATATCTGCTGCTTTCTTTT 15 13 1 GCGCATCGCT 0.945003 -125 *** * *** *** Masking position 8 Map Score: 50.0142 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 49 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 ATTTTTATTAAAAAAGATAAAATTATTATTGA 4 65 1 AAAAAGTAAA 0.925799 -166 CTCTATTCCTAAACAGCAACATCATACAAGAA 4 151 1 AAACAGAAAT 0.63822 -80 TGATACCATCAAAAAGTTATAATTGGTACTTT 5 28 1 AAAAAGTAAA 0.925799 -79 ATGATTACTTAAAATGATAGCAGACCCGGCCA 6 26 0 AAAATGTACA 0.702764 -43 TAAGATTACAAAAAAGGTAAAAAAACCAAATC 8 131 1 AAAAAGTAAA 0.925799 -170 AAGTACTATAAAACTGTAACAAAAAAAGACCT 11 28 0 AAACTGAAAA 0.887006 -127 ACATTTTACGAAAATGAAATAAAAGTACTATA 11 50 0 AAAATGAAAA 0.960937 -105 TCATTTTCGTAAAATGTAACAAAATTACTTGA 11 65 1 AAAATGAAAA 0.960937 -90 CAAGGCGGACAAAAATAAAAAATCCCCCTGCC 12 35 0 AAAAATAAAA 0.659271 -59 TTTTTAACAAAAAAAGAAAGCAGCAGATATGC 15 26 0 AAAAAGAACA 0.929674 -112 TTTTTTTGTTAAAAAGCAAAAATAAACAAAAA 15 43 1 AAAAAGAAAA 0.976429 -95 ATTCAAAAACAAACAGAAATCATATATAATGA 15 77 1 AAACAGAACA 0.808374 -61 GGTTTAATAAAAAAACTAAAAAAAACACCCAA 16 39 0 AAAAACAAAA 0.74145 -75 ATATACAGCAAAAAAGAAGAAATTTAACAAAA 17 50 0 AAAAAGAGAA 0.929674 -76 GGGTAGCATAAAAAAGGAGAAATGAATG 17 108 1 AAAAAGAGAA 0.929674 -18 AATGGAGGAAAAAATGAAAAATAGTTCTAAAT 18 87 0 AAAATGAAAT 0.766507 -90 AATTACATTGAAAATGGAGGAAAAAATGAAAA 18 99 0 AAAATGAGAA 0.887006 -78 AATGAAAGTTAAAAAGGCAGAAGACAGCCAAA 19 56 1 AAAAAGCAAA 0.848956 -102 TTTAAAATAAAAAATGGAAGAAGTTCTTTTTG 19 84 0 AAAATGAAAA 0.960937 -74 ****** ** ** Masking position 3 Map Score: 23.418 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 197 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 TGTGCCGCATCCGGCAATCAATGCCTGATGC 1 34 0 CCGGCATCAA 0.966622 -267 AGTGCCTTATCCGGCCTACAGGTCGGCAACA 1 65 1 CCGGCCACAG 0.991855 -236 CGCGTCTTATCAGGCCTACAACTGTTGCCGA 1 87 0 CAGGCCACAA 0.984883 -214 TTGTGCGCATCCGGCAATCAATGCCTGATGC 1 126 0 CCGGCATCAA 0.966622 -175 AGTCGCTTATCAGGCCTACAGGTCGGCAATA 1 156 1 CAGGCCACAG 0.977374 -145 CGCGTCTTATCAGGCCTACAACTATTGCCGA 1 178 0 CAGGCCACAA 0.984883 -123 GCGCGCATCCACGGCAATCAATGCCTGATGC 1 217 0 ACGGCATCAA 0.882457 -84 AGCGCCTTATCCGGCCTACGGGTCGTGCATC 1 249 1 CCGGCCACGG 0.981845 -52 ACCGAATTTACAGGAACACAGAAC 1 287 1 CAGGAAACAG 0.80816 -14 TAACAATCGGCCGCCCGACAATACTGGAGAT 3 15 0 CCGCCCACAA 0.943173 -270 TGATTATTCGCCGGAACACAAAAAGAGCTGC 7 47 0 CCGGAAACAA 0.947202 -76 GGTCTTTTTGACGGCAAACGAAAACCCTCCC 10 28 0 ACGGCAACGA 0.921905 -78 TCATCATAACAAGGCGGACAAAAATAAAAAA 12 45 0 AAGGCGACAA 0.736515 -49 AAAATATAAGACGGACTACGATATGAGGAAG 14 26 1 ACGGACACGA 0.799152 -31 ****** **** Masking position 9 Map Score: 21.5316 Number of sites scoring better than the average of aligned sites = 937 Number in coding regions = 629 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 TGATAAGACGCGACAGCGTCGCATCAGGCA 1 14 1 CGACAGCGTC 0.969261 -287 GCCTACAGGTCGGCAACAGTTGTAGGCCTG 1 78 1 CGGCAACAGT 0.837914 -223 TGATAAGACGCGACAGCGTCGCATCAGGCA 1 106 1 CGACAGCGTC 0.969261 -195 TGATAAGACGCGACAGCGTCGCATCAGGCA 1 197 1 CGACAGCGTC 0.969261 -104 GTCGTGCATCCGACAACACCGAATTTACAG 1 270 1 CGACAACACC 0.894442 -31 GCCGTGTTGACGACATCAGGAGGCCAGT 2 9 0 CGACATCAGG 0.840533 -279 GCCAGTAAATCGACAACGGCGGCAACAGGC 3 186 1 CGACAACGGC 0.96981 -99 AAAGGTTAATCGACAGCACGATTTTTACAC 3 217 1 CGACAGCACG 0.972339 -68 ACCACCACACCGACAGGAGGCATCCC 4 215 1 CGACAGGAGG 0.961247 -16 AAGAAAATACCGACAGGGGGATATTCAC 5 89 1 CGACAGGGGG 0.982076 -18 CCGGAAAATCCGGCAGCTCTCAGGAGCGTG 7 18 0 CGGCAGCTCT 0.820122 -105 CCGGATTTTCCGGCAGCTCTTTTTGTGTTC 7 35 1 CGGCAGCTCT 0.820122 -88 GCCGTTATTTCGGCAAGGGGATTGCAG 12 8 0 CGGCAAGGGG 0.934762 -86 GCCGAAATAACGGCAGGGGGATTTTTTATT 12 24 1 CGGCAGGGGG 0.980333 -70 ********** Masking position 5 Map Score: 19.4484 Number of sites scoring better than the average of aligned sites = 2777 Number in coding regions = 2671 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 TGTCAGTAACGAGAAGGTCGCGAATTCAGGCG 2 225 1 GAGAAGTGCG 0.785841 -63 ATGGTTTTGCAGGAAAATGCCCGAGATGTGAA 3 127 1 AGGAAATCCC 0.719999 -158 TTTAGGAATAGAGAAAGCAGACCGTTATTTGT 4 132 0 GAGAAACGAC 0.840464 -99 AACATCATACAAGAAATCCCCCAAAATCATGC 4 168 1 AAGAAACCCC 0.976157 -63 GTATCAGAAGGAGAAACTACAAA 5 2 0 GAGAAATCAA 0.487532 -105 TCATACCAAAGAGAAGTCAGAATGATAAGAAA 5 63 1 GAGAAGCGAA 0.537598 -44 TCAGAATGATAAGAAAATACCGACAGGGGGAT 5 79 1 AAGAAATCCG 0.867299 -28 TCATTGGAAAGAAAATGGCCGGGTCTGCTA 6 9 1 AAGAAATGCC 0.953867 -60 TACATTTTGAAAGAAGGTTCCCCAACA 7 106 1 AAGAAGTCCC 0.945631 -17 TAAGGCAAATGAGAAATTTCCCGCTCTATGGG 8 172 1 GAGAAATCCC 0.92575 -129 ATGAAATTCCCCCATTTTCGAA 9 1 1 ATGAAATCCC 0.634311 -64 GTTTGCCGTCAAAAAGACCGCCATAGTAAAGT 10 40 1 AAAAAGCGCC 0.829711 -66 GGACAAAAATAAAAAATCCCCCTGCCGTTATT 12 29 0 AAAAAACCCC 0.876847 -65 TGAAACGAGAAAGCGGCATATCTGCTGC 15 7 1 GAGAAACGCA 0.898069 -131 TTAACAAAAAAAGAAAGCAGCAGATATGCCGC 15 23 0 AAGAAACGCA 0.914814 -115 AAAAAAACTAAAAAAAACACCCAAGCGCAACA 16 31 0 AAAAAACCCC 0.876847 -83 TTTACCATATAAAAAAACAGCGCTTTGATAGC 18 26 0 AAAAAACGCG 0.646711 -151 AAATTATTGAAAGAAGGTTCAAAAGGAA 18 159 1 AAGAAGTCAA 0.468051 -18 GTTAAAAAGGCAGAAGACAGCCAAAAAGAACT 19 63 1 CAGAAGCGCC 0.815465 -95 ****** * *** Masking position 5 Map Score: 12.9468 Number of sites scoring better than the average of aligned sites = 1678 Number in coding regions = 1463 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 6 GACAGCACGATTTTTACACTCATCTCGTCGGAGATGTGACG 3 228 1 TTTCATGTGG 0.603012 -57 TCAGTTATAATGGTTTGGAACAGATAGGAGGGGCAAAG 4 8 0 TTTGATGGGG 0.860243 -223 TTTCAAAATGTATTTGCTGTTATTTTGGCTGGAATTGTTGT 7 77 0 TTTCATGGTG 0.829554 -46 ATAAATGGAATTGTAAACGTTATCAAGGAGGTCGTCAT 8 273 1 TTAAAAGGGG 0.9802 -28 TTATATACAATTACAGATTCGAAAATGGGGGAATTTCAT 9 9 0 TCAAAAGGGG 0.93002 -56 TAATTGTATATAATAGAAAGAAAATGGGGGGATCTGAT 9 37 1 TTAAATGGGG 0.977552 -28 GATTGTCTCTTTCTTTACTTTACTATGGCGGTCTTTTTGAC 10 47 0 TTTAAAGGGG 0.971059 -59 ATTAAGTAAGTGATAACATTTATCAAGGAGGATAAA 11 129 1 TTACAAGGGG 0.978274 -26 ACAAGTTGGTTCTCTCATCATAACAAGGCGGACAAAAATAA 12 49 0 TCTAAAGGGG 0.900074 -45 TCCTTTTTTATGCTACCCTTCATATCGGCTGGAAATGGGTA 17 85 0 TTACATGGTG 0.877764 -41 ATCTTCCTTTAAATTACATTGAAAATGGAGGAAAAAATGAA 18 101 0 ATTCAAGGGG 0.841181 -76 TCTTTCAATAATTTACAAATTATATCGGCGGATCTTCCTTT 18 132 0 ATAAATGGGG 0.883148 -45 TCTTTGCATATCTTATAAAAAACAAGGGGGGCTAAAC 19 7 0 TTAAAAGGGG 0.9802 -151 CTTAAAAAAGTTTTAAAATAAAAAATGGAAGAAGTTCTTTT 19 86 0 TTAAAAGGAG 0.780319 -72 CCTTCAGGTTTGATACAGTATATATCGGCTGCTTAAAAAAG 19 117 0 TTAAATGGTG 0.887577 -41 * ** * * * ** ** Masking position 12 Map Score: 14.8057 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 147 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 ATGCGACGCTGTCGCGTCTTATCAGGC 1 8 0 GTCGCGTCTT 0.986132 -293 ACGCGACAGCGTCGCATCAGGCATTGATTG 1 21 1 GTCGCATCAG 0.965686 -280 ATGCGACGCTGTCGCGTCTTATCAGGCCTA 1 100 0 GTCGCGTCTT 0.986132 -201 ACGCGACAGCGTCGCATCAGGCATTGATTG 1 113 1 GTCGCATCAG 0.965686 -188 ATGCGCACAAGTCGCTTATCAGGCCTACAG 1 147 1 GTCGCTTATC 0.75861 -154 ATGCGACGCTGTCGCGTCTTATCAGGCCTA 1 191 0 GTCGCGTCTT 0.986132 -110 ACGCGACAGCGTCGCATCAGGCATTGATTG 1 204 1 GTCGCATCAG 0.965686 -97 TAACGAGAAGGTCGCGAATTCAGGCGCTTT 2 231 1 GTCGCGAATT 0.738433 -57 ATCATTTTTCGTCGCGTCACATCTCCGACG 3 253 0 GTCGCGTCAC 0.98846 -32 GAGATAGCTCGTCCCGTAACACGTTTGGCG 8 238 0 GTCCCGTAAC 0.758275 -63 ********** Masking position 2 Map Score: 14.4374 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 142 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 TAGCATGATTTTGGGGGATTTCTTGTATGA 4 172 0 TTGGGGGATT 0.5775 -59 ATGGTATCAGAAGGAGAAACTACAAA 5 7 0 AAGGAGAAAC 0.37303 -100 AAAATACCGACAGGGGGATATTCAC 5 92 1 CAGGGGGATA 0.806835 -15 AGATTCGAAAATGGGGGAATTTCAT 9 6 0 ATGGGGGAAT 0.945286 -59 TAGAAAGAAAATGGGGGGATCTGAT 9 50 1 ATGGGGGGAT 0.888277 -15 CCCTCCCGAAAAGGAGGGCAGTCT 10 5 0 AAGGAGGGCA 0.84172 -101 AACATTTATCAAGGAGGATAAA 11 143 1 AAGGAGGATA 0.905387 -12 GAAATAACGGCAGGGGGATTTTTTATTTTT 12 27 1 CAGGGGGATT 0.867317 -67 TCATCATAACAAGGCGGACAAAAATAAAAA 12 46 0 AAGGCGGACA 0.754259 -48 ATAAAAGGGTATGGAGGAATATCAAAT 15 121 1 ATGGAGGAAT 0.925954 -17 ATTTATCTTAAAGGAGGAGTCAACGAGA 16 96 1 AAGGAGGAGT 0.870907 -18 TAGCATAAAAAAGGAGAAATGAATG 17 111 1 AAGGAGAAAT 0.718031 -15 TACATTGAAAATGGAGGAAAAAATGAAAAA 18 98 0 ATGGAGGAAA 0.888773 -79 TATAAAAAACAAGGGGGGCTAAAC 19 5 0 AAGGGGGGCT 0.919988 -153 ********** Masking position 6 Map Score: 6.19267 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 211 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 9 TCAGGCATTGATTGCCGGATGCGGCACAAGTGCC 1 37 1 ATTGCCGAGG 0.951425 -264 TCAGGCATTGATTGCCGGATGCGCACAAGTCGCT 1 129 1 ATTGCCGAGC 0.99028 -172 TCAGGCATTGATTGCCGTGGATGCGCGCGAGCGC 1 220 1 ATTGCCGGGC 0.99733 -81 CATCTCCAGTATTGTCGGGCGGCCGATTGTTAAT 3 14 1 ATTGTCGGCC 0.903037 -271 GCCGATTGTTAATGCCGCGTAAGCAGTTGGTTCA 3 35 1 AATGCCGGGC 0.993882 -250 TCACCCACTTAATGCCGTGATTGCCAGTAAATCG 3 164 1 AATGCCGGGC 0.993883 -121 TGGAAAGAAAATGGCCGGGTCTGCTATCATTTTA 6 15 1 ATGGCCGGGC 0.991373 -54 ******* * ** Masking position 1 Map Score: 7.00968 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 158 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ATTCACGCTGTATCTTGAAAAATCGACGTTT 2 98 0 TATTTGAAAA 0.757877 -190 TTTTATCTTTTTTAATAAAAATTTATTTTTC 4 56 0 TTTATAAAAA 0.856934 -175 TTCTCTTTGGTATGATGAAAAGTACCAATTA 5 47 0 TATATGAAAA 0.938749 -60 CATTTTAAGTAATCATGAAAAGAAAGGAATG 6 42 1 AATATGAAAA 0.619916 -27 CCCTTCCAATTCTTATGAAAAGGTTCTTTTG 8 64 0 TCTATGAAAA 0.868246 -237 TGTAATTGTATATAATAGAAAGAAAATGGGG 9 35 1 TATATAGAAA 0.703462 -30 ATATATGCTATGATAAAAATATAAGACGG 14 9 1 TATATAAAAA 0.937658 -48 GCTTTCTTTTTTTGTTAAAAAGCAAAAATAA 15 37 1 TTTTTAAAAA 0.549886 -101 AGAAATCATATATAATGAAAACGGATACAAA 15 91 1 TATATGAAAA 0.938749 -47 GGATAAAAGGTTTAATAAAAAAACTAAAAAA 16 48 0 TTTATAAAAA 0.856934 -66 ATATGAAGGGTAGCATAAAAAAGGAGAAATG 17 101 1 TAGATAAAAA 0.720827 -25 TCTTTGCATATCTTATAAAAAACAAGGGGGG 19 17 0 TCTATAAAAA 0.866059 -141 AAAAAAGTTTTAAAATAAAAAATGGAAGAAG 19 93 0 TAAATAAAAA 0.635316 -65 *** ******* Masking position 9 Map Score: 7.79437 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 101 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 11 TAAGCGACTTGTGCGCATCCGGCAATCAAT 1 135 0 GTGCGCATCC 0.974012 -166 TAAGGCGCTCGCGCGCATCCACGGCAATCA 1 228 0 GCGCGCATCC 0.992772 -73 GGCCTACGGGTCGTGCATCCGACAACACCG 1 261 1 TCGTGCATCC 0.943298 -40 CTTTGCCCCTCCTATCTGTTCC 4 3 1 TTGCCCCTCC 0.850875 -228 GCTCTCAGGAGCGTGCATTCTT 7 3 0 GCGTGCATTC 0.829372 -120 AAGTGAATATACGCCCTTCCAATTCTTATG 8 78 0 ACGCCCTTCC 0.961367 -223 CGGTAACGCCCTTCCTCATATCGTA 14 42 0 ACGCCCTTCC 0.961367 -15 ********** Masking position 8 Map Score: 2.26715 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 331 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 TCCTGCAAAACCATACCCTTACGAAAAGTA 3 111 0 CCATACCCTT 0.984549 -174 CCTATCTGTTCCAAACCATTATAACTGAAA 4 21 1 CCAAACCATT 0.941306 -210 GTAAAAGCCTCCAAACCCCTTTTTACTCGA 10 86 0 CCAAACCCCT 0.973942 -20 TGATATTCCTCCATACCCTTTTATTTGTAT 15 115 0 CCATACCCTT 0.984549 -23 ********** Masking position 5 Map Score: 1.51078 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 13 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 GATGTCGTCAACACGGCGAAATAGTAATCAC 2 22 1 AACGGCGAAA 0.482786 -266 TTACGTGGTTTTCCGTCGAAAATTTAAGGTA 2 66 0 TCCGTCGAAA 0.893606 -222 TTTCATTACGACCAGTCTAAAAAGCGCCTGA 2 250 0 ACAGTCTAAA 0.440306 -38 CAACGGCGGCAACAGGCGAAAGGTTAATCGA 3 199 1 ACAGGCGAAA 0.926529 -86 CATACAAGAAATCCCCCAAAATCATGCTACA 4 173 1 ACCCCCAAAA 0.585326 -58 TCTTTTTGTGTTCCGGCGAATAATCACAACA 7 52 1 TCCGGCGAAT 0.559035 -71 TCACAACAATTCCAGCCAAAATAACAGCAAA 7 75 1 TCAGCCAAAA 0.917439 -48 GGTTTTCGTTTGCCGTCAAAAAGACCGCCAT 10 33 1 TCCGTCAAAA 0.769867 -73 AAAAAAAGAAAGCAGCAGATATGCCGCTTTC 15 19 0 ACAGCAGATA 0.611337 -119 GGTAAATATATACAGCAAAAAAGAAGAAATT 17 58 0 TCAGCAAAAA 0.56344 -68 TTTACCCATTTCCAGCCGATATGAAGGGTAG 17 83 1 TCAGCCGATA 0.921187 -43 TTAAAGGAAGATCCGCCGATATAATTTGTAA 18 130 1 ACCGCCGATA 0.94234 -47 AAAGGCAGAAGACAGCCAAAAAGAACTTCTT 19 68 1 GCAGCCAAAA 0.773716 -90 AACTTTTTTAAGCAGCCGATATATACTGTAT 19 115 1 ACAGCCGATA 0.931236 -43 * ********* Masking position 9 Map Score: 2.73393 Number of sites scoring better than the average of aligned sites = 1960 Number in coding regions = 1805 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 14 AGACGCGACAGCGTCGCATCAGGCATTGATTG 1 19 1 GCTCGCATCG 0.995999 -282 AGACGCGACAGCGTCGCATCAGGCATTGATTG 1 111 1 GCTCGCATCG 0.995999 -190 AGACGCGACAGCGTCGCATCAGGCATTGATTG 1 202 1 GCTCGCATCG 0.995999 -99 AATGCGGTGAGCATCACATCACCACAATTCAG 2 137 1 GCTCACATCC 0.993725 -151 TGGGTGATTTGCTTCACATCTCGGGCATTTTC 3 139 0 GCTCACATCC 0.993725 -146 ATTTTTCGTCGCGTCACATCTCCGACGAGATG 3 248 0 GCTCACATCC 0.993724 -37 ** ******* * Masking position 8 Map Score: 13.5297 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 25 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 15 GTTCTGTGTTCCTGTAAATTCGGTGTTGT 1 282 0 TTCCTTAAAT 0.955658 -19 GGTCAGGTTCTTACCTTAAATTTTCGACGGA 2 55 1 TTACCTAAAT 0.87654 -233 CTCACCGCATTTCCTGAAAATTCACGCTGTA 2 117 0 TTCCTAAAAT 0.943025 -171 ATACAAGAAATCCCCCAAAATCATGCTACAC 4 174 1 TCCCCAAAAT 0.860143 -57 CTTTTCATGATTACTTAAAATGATAGCAGAC 6 33 0 TTACTAAAAT 0.818682 -36 AGTAACTAATTTCCCATAAATAAATAGTATT 17 20 0 TTCCCTAAAT 0.962999 -106 TCGGCGGATCTTCCTTTAAATTACATTGAAA 18 118 0 TTCCTTAAAT 0.955658 -59 ***** ***** Masking position 8 Map Score: 3.08501 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 44 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925